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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1316/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifcounter 1.30.0  (landing page)
Wolfgang Kopp
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/motifcounter
git_branch: RELEASE_3_20
git_last_commit: b49cf20
git_last_commit_date: 2024-10-29 10:18:10 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for motifcounter on lconway

To the developers/maintainers of the motifcounter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifcounter.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: motifcounter
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.30.0.tar.gz
StartedAt: 2024-11-20 00:15:05 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:21:33 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 387.4 seconds
RetCode: 0
Status:   OK  
CheckDir: motifcounter.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .zenodo.json
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘motifcounter’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
simulateClumpSizeDist 10.14  0.324  10.496
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck/00check.log’
for details.


Installation output

motifcounter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifcounter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roption.c -o Roption.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
    int mins, maxs, noscores;
                    ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c background.c -o background.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain_single.c -o markovchain_single.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix.c -o matrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c overlap.c -o overlap.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score1d.c -o score1d.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score2d.c -o score2d.o
score2d.c:597:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
    double p, p0 = 0.0, p1 = 0.0, ptmp;
                        ^
score2d.c:597:15: warning: variable 'p0' set but not used [-Wunused-but-set-variable]
    double p, p0 = 0.0, p1 = 0.0, ptmp;
              ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
    int j, i, index, cindex, ds;
                     ^
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  int s, index, cindex;
                ^
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
    int s, index, cindex;
                  ^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c sequence.c -o sequence.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c simulate.c -o simulate.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-motifcounter/00new/motifcounter/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (motifcounter)

Tests output

motifcounter.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(motifcounter)
> 
> test_check("motifcounter")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
> 
> proc.time()
   user  system elapsed 
 75.255   1.728  77.390 

Example timings

motifcounter.Rcheck/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.1270.0080.136
combinatorialDist0.1850.0110.197
compoundPoissonDist0.1330.0170.151
computeClumpStartProb0.0860.0030.089
generateDNAString0.0630.0020.065
generateDNAStringSet0.0940.0020.097
hitStrand0.0610.0070.070
lenSequences0.0640.0110.077
markovModel0.0780.0020.081
motifAndBackgroundValid0.0560.0020.058
motifEnrichment1.8010.0161.821
motifHitProfile0.0600.0030.064
motifHits0.0640.0040.068
motifValid0.0020.0010.003
motifcounter-package0.6610.0130.677
motifcounterOptions000
normalizeMotif0.0010.0010.002
numMotifHits0.4330.0080.443
probOverlapHit0.1080.0030.112
readBackground0.0620.0030.065
revcompMotif0.0020.0000.002
scoreDist0.0600.0010.062
scoreDistBf0.0740.0020.076
scoreDistEmpirical1.8140.0251.850
scoreHistogram0.1500.0070.158
scoreHistogramSingleSeq0.0660.0060.073
scoreProfile0.3200.0040.327
scoreSequence0.0580.0030.061
scoreStrand0.0600.0020.063
scoreThreshold0.0550.0010.057
sigLevel000
simulateClumpSizeDist10.140 0.32410.496
simulateNumHitsDist1.2660.0301.302